run_metadata: 52926
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 52926 | SRR13046869 | SRX6369532 | SRS5030899 | SRP212161 | PRJNA551383 | Defining codon mediated mRNA decay and No go decay in zebrafish embryos | GSE133392 | Other | The control of mRNA stability plays a central role in regulating gene expression patterns. While much is known about the roles of 5´ and 3´ untranslated regions in the mRNA stability control the impact of protein coding sequences on mRNA stability had been obscure. Recently several groups reported that codon composition in the ORF affects mRNA deadenylation and degradation rates in a translation dependent manner. Hence codons define not only the amino acid sequences to be synthesized but also the stability of mRNAs. However how 61 codons differently affect mRNA stability remains unclear. Besides aberrant stalling of the ribosome induces ribosome quality control RQC and No go decay. The relationship between the two co translational mRNA decay pathways is not systematically analyzed. To precisely characterize the effects of 61 codons on mRNA stability we developed a simplified reporter system that allows detection of the effect of every single codon on mRNA stability in zebrafish embryos. Using this system we show that the effect of codons on mRNA stability is partially but significantly correlated with the translation elongation rate and tRNA abundance. Interestingly the codon effect is still maintained in zebrafish embryos lacking Znf598 an essential mediator of RQC and NGD. Znf598 dependent NGD targets a particular type of ribosome stalling but has limited impact on endogenous mRNA stability. Our study thus defines two related co translational mRNA decay pathways during animal development. Overall design: Ribosome profiling | pubmed:32375038 | zebrafish monosome rep2 | GSM3907594 | tissue:whole embryo|treatment:injected with sfGFP mRNAs at xxx cell stage|genotype:WT|developmental stage:4 hpf embryo|strain:AB strain | zebrafish monosome rep2 | Library strategy: Ribo Seq Basecalling with Illumina Casava 1.8 software three prime adapter trimming with FastX toolkit Library sorting based on sample barcode sequence with custom script random barcode triming with custom script rRNA and other non coding RNA alignment with bowtie2 v2.1.0 Alignment with TopHat v2.0.9 Read quantitation using custom scripts Genome build: GRCz11 Supplementary files format and content: text files contain three columns: 1. transcript name;2. CDS region nt used for read counting;3. read counts | whole embryo | injected with sfGFP mRNAs at xxx cell stage | Rnase I footprinting ribosome pelleting RNA extraction RNA extraction preadenylated linker ligation rRNA depeletion reverse transcription cDNA circularization PCR amplification for ribosome profiling | cultured with standard system water at 28.5 degree cultured with standard system water at 28.5 degree | treatment:injected with sfGFP mRNAs at xxx cell stage|genotype:WT|developmental stage:4 hpf embryo|strain:AB strain | GSM3907594 | GSM3907594: zebrafish monosome rep2; Danio rerio; OTHER | GSM3907594 | 1 | Rnase I footprinting ribosome pelleting RNA extraction RNA extraction preadenylated linker ligation rRNA depeletion reverse transcription cDNA circularization PCR amplification for ribosome profiling | GEO Accession:GSM3907594 | OTHER | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP212161 | zebrafish_monosome_rep2.fastq | fastq | 2459268347.0 | 82029289.0 | GSM3907594 r11 | 0:29.98 1:0 | A:546542098;C:687582771;G:747645444;T:477498034;N:0 | 29 | 0 | 546542098 | 687582771 | 747645444 | 477498034 | 0 | SRX6369532 | SRS5030899 | SRA914456 | GEO | Riken | 1 | 0.86891 | 0.37383 | 0.88745 | 0.88442 | 35 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | Japan | 2019-06-27 | Blastula | Embryo | Whole Organism | All anatomical structures |